My car had that problem, but the check engine light flashing can be soooo many different things. It could be the 02 sensors, but for me it was the EGR valve. I fixed it by trial and error but my 5.0 was runnin into quite a few problems with performance. I suggest not worrying about it until it starts to affect the way the car runs. A couple of free mods that theoretically will help is to reroute the water hose that goes into your TB (keeps air cooler) and you could take out your air silencer inside the fender well. Other than that i think you have most of the cheap mods covered. Hope thats of some help.
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98 Cobra, CAI, Flowmasters, o/r h-pipe. 4.10s, Hurst shifter.
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